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- PDB-3o2k: Crystal Structure of Brevianamide F Prenyltransferase Complexed w... -

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Basic information

Entry
Database: PDB / ID: 3o2k
TitleCrystal Structure of Brevianamide F Prenyltransferase Complexed with Brevianamide F and Dimethylallyl S-thiolodiphosphate
ComponentsBrevianamide F prenyltransferase
KeywordsTRANSFERASE / PT Barrel / Brevianamide F Prenyltransferase
Function / homology
Function and homology information


tryprostatin B synthase / tryptophanyl aminopeptidase / verruculogen biosynthetic process / prenyltransferase activity / aminopeptidase activity / proteolysis
Similarity search - Function
Aromatic prenyltransferase DMATS-type, fungi / Aromatic prenyltransferase, DMATS-type / Tryptophan dimethylallyltransferase / Aromatic prenyltransferase
Similarity search - Domain/homology
DIMETHYLALLYL S-THIOLODIPHOSPHATE / Chem-QRP / Tryprostatin B synthase ftmPT1 / Tryprostatin B synthase ftmPT1
Similarity search - Component
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsJost, M. / Zocher, G.E. / Stehle, T.
CitationJournal: J.Am.Chem.Soc. / Year: 2010
Title: Structure-function analysis of an enzymatic prenyl transfer reaction identifies a reaction chamber with modifiable specificity.
Authors: Jost, M. / Zocher, G. / Tarcz, S. / Matuschek, M. / Xie, X. / Li, S.M. / Stehle, T.
History
DepositionJul 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Oct 2, 2019Group: Data collection / Non-polymer description / Structure summary
Category: chem_comp / entity
Item: _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight
Revision 2.1Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Brevianamide F prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7106
Polymers53,8991
Non-polymers8125
Water82946
1
A: Brevianamide F prenyltransferase
hetero molecules

A: Brevianamide F prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,42112
Polymers107,7982
Non-polymers1,62310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3350 Å2
ΔGint-46 kcal/mol
Surface area31940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.770, 82.770, 124.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Brevianamide F prenyltransferase


Mass: 53898.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Gene: ftmPT1 / Plasmid: pQE70 / Production host: Escherichia coli (E. coli) / Strain (production host): XL-1 Blue MRF / References: UniProt: Q4G2I1, UniProt: Q4WAW7*PLUS

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Non-polymers , 5 types, 51 molecules

#2: Chemical ChemComp-DST / DIMETHYLALLYL S-THIOLODIPHOSPHATE / DMASPP / DMAPP / DMADP / Dimethylallyl pyrophosphate / dimethylallyl diphosphate / isoprenyl pyrophosphate


Mass: 262.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O6P2S
#3: Chemical ChemComp-QRP / (3S,8aS)-3-(1H-indol-3-ylmethyl)hexahydropyrrolo[1,2-a]pyrazine-1,4-dione / Brevianamide F / cyclo-L-Trp-L-Pro


Mass: 283.325 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H17N3O2
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.3M ammonium sulfate, 0.2M lithium sulfate, 0.1M MES, VAPOR DIFFUSION, HANGING DROP. Stepwise transferred to 1.3M lithium sulfate, 0.1M MES pH 6.5, 2.5mM brevianamide F, 10mM dimethylallyl ...Details: 1.3M ammonium sulfate, 0.2M lithium sulfate, 0.1M MES, VAPOR DIFFUSION, HANGING DROP. Stepwise transferred to 1.3M lithium sulfate, 0.1M MES pH 6.5, 2.5mM brevianamide F, 10mM dimethylallyl S-thiolodiphosphate for soaking, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. all: 17531 / Num. obs: 17518 / % possible obs: 99.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 23.6 % / Biso Wilson estimate: 50.1 Å2 / Rmerge(I) obs: 0.042 / Rsym value: 0.109 / Net I/σ(I): 29.95
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 27 % / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 8.61 / Num. unique all: 1258 / Rsym value: 0.407 / % possible all: 100

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Processing

Software
NameClassification
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3O24

3o24


Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.94 / SU B: 19.944 / SU ML: 0.211 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 0.574 / ESU R Free: 0.262 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23451 874 5 %imported from native structure, random extension to full resolution
Rwork0.20534 ---
all0.209 17531 --
obs0.20681 16613 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 58.076 Å2
Baniso -1Baniso -2Baniso -3
1--4.51 Å20 Å20 Å2
2---4.51 Å2-0 Å2
3---9.03 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3393 0 49 46 3488
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0223541
X-RAY DIFFRACTIONr_bond_other_d0.0010.022395
X-RAY DIFFRACTIONr_angle_refined_deg0.8251.9674827
X-RAY DIFFRACTIONr_angle_other_deg0.74635782
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.735426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.1822.945163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.02415527
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2091525
X-RAY DIFFRACTIONr_chiral_restr0.0480.2517
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213942
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02773
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.59742154
X-RAY DIFFRACTIONr_mcbond_other0.1314856
X-RAY DIFFRACTIONr_mcangle_it1.0514.53472
X-RAY DIFFRACTIONr_scbond_it0.97461387
X-RAY DIFFRACTIONr_scangle_it1.4986.51355
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 62 -
Rwork0.258 1176 -
obs-1259 100 %
Refinement TLS params.Method: refined / Origin x: -19.5448 Å / Origin y: 17.4432 Å / Origin z: 0.9004 Å
111213212223313233
T0.1439 Å2-0.0255 Å2-0.045 Å2-0.1665 Å20.0359 Å2--0.038 Å2
L2.1674 °2-0.862 °20.1801 °2-1.7567 °2-0.3994 °2--0.7715 °2
S-0.0202 Å °-0.1499 Å °0.0297 Å °-0.0953 Å °0.1062 Å °0.1389 Å °-0.1041 Å °-0.1275 Å °-0.086 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 456
2X-RAY DIFFRACTION1A475 - 477
3X-RAY DIFFRACTION1A478 - 525

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